Issues

• tasks/ is tracked on main; it should be gitignored

  scverse/mantispy#185 · Filter by author timtreis opened on Oct 4, 2026

• Backlog: agreed method work packages not yet filed as issues

  scverse/mantispy#179 · Filter by author timtreis opened on Oct 1, 2026

• Modify img that gets loaded in text preview so that it doesn't crop the logo

  Enhancement

  scverse/mantispy#177 · Filter by author timtreis opened on Sep 30, 2026

• Tutorial: pooled_rare (pre-aggregated barcode-resolution input)

  scverse/mantispy#165 · Filter by author timtreis opened on Sep 28, 2026

• Tutorial: chroma (non-standard dye channels)

  scverse/mantispy#164 · Filter by author timtreis opened on Sep 28, 2026

• Reprocess the Funk 2022 optical pooled screen into shareable cell-level data objects (for the publication)

  scverse/mantispy#141 · Filter by author timtreis opened on Sep 26, 2026

• OPS documentation section: tutorials for optical pooled screening analysis (epic)

  scverse/mantispy#140 · Filter by author timtreis opened on Sep 26, 2026
  1

• Validate the cell-resolution hit-calling module on real OPS data (specificity, sensitivity, UX)

  scverse/mantispy#139 · Filter by author timtreis opened on Sep 26, 2026

• Add an optical pooled screening (OPS) cell-resolution dataset to mt.ds (Funk 2022 essential genes)

  scverse/mantispy#138 · Filter by author timtreis opened on Sep 26, 2026
  3

• subpopulation_hits has the same cell-within-well pseudoreplication as hit_calling (#68 follow-up)

  scverse/mantispy#137 · Filter by author timtreis opened on Sep 26, 2026

• Curated feature->process priors for enrich do not cleanly pay off (prototype); enrich channel/feature_group scoring is the interpretable value

  scverse/mantispy#134 · Filter by author timtreis opened on Sep 26, 2026

• feature_select: helper to choose decorr_threshold by a user-supplied metric

  scverse/mantispy#133 · Filter by author timtreis opened on Sep 25, 2026

• No way to name a learned embedding's axes from a named feature block on the same wells

  scverse/mantispy#110 · Filter by author timtreis opened on Sep 21, 2026

• noise_removal's stdev_cutoff cannot be used with the normalization the package recommends

  scverse/mantispy#109 · Filter by author timtreis opened on Sep 21, 2026

• The schema requires CellProfiler var columns of every object, including those with no such features

  scverse/mantispy#104 · Filter by author timtreis opened on Sep 20, 2026

• Nothing in the repository regenerates registry.yaml

  scverse/mantispy#96 · Filter by author timtreis opened on Sep 20, 2026

• The CI data cache has no size budget, and the 10 GB limit fails quietly

  scverse/mantispy#95 · Filter by author timtreis opened on Sep 20, 2026

• jump_target2 cannot be asked for a plate from particular sources

  scverse/mantispy#94 · Filter by author timtreis opened on Sep 20, 2026

• Multi-plate profiles are read one file at a time

  scverse/mantispy#93 · Filter by author timtreis opened on Sep 20, 2026

• import mantispy parses the whole dataset registry, even when no dataset is loaded

  scverse/mantispy#92 · Filter by author timtreis opened on Sep 20, 2026

• composition_dispersion is not a reserved uns name, and hit_calling's Raises is out of date

  scverse/mantispy#91 · Filter by author timtreis opened on Sep 20, 2026

• hitcall is not checked numerically against tcplfit2

  scverse/mantispy#90 · Filter by author timtreis opened on Sep 20, 2026

• The OASIS plate-map join duplicates _join_platemap and loses its validation

  scverse/mantispy#86 · Filter by author timtreis opened on Sep 20, 2026

• Document each shipped dataset: derived columns, stats, and the scripts that rebuild it

  documentation
  scverse/mantispy#74 · Filter by author timtreis opened on Sep 18, 2026

• Cell-resolution tests treat cells within a well as independent replicates

  scverse/mantispy#68 · Filter by author timtreis opened on Sep 18, 2026